CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Abstract

Summary Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced ChIA-PET strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CTCF and RNAPII with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes towards CTCF-foci for coordinated transcription. Furthermore, we show that haplotype-variants and allelic-interactions have differential effects on chromosome configuration influencing gene expression and may provide mechanistic insights into functions associated with disease susceptibility. 3D-genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D-genome strategy thus provides unique insights in the topological mechanism of human variations and diseases.

Topologically-associating domains: gene warehouses adapted to serve transcriptional regulation

“…Indeed, it has been recently observed that in chromatin loops formed by convergent CBS (convergent loops), forward and reverse CBSs are strongly associated with forward and reverse TSS, respectively, and TSS peaks are preferentially located downstream of the forward CBS and upstream of the reverse CBS. 17 One may note that the above-proposed interpretation of the extrusion model of TAD formation makes this model similar to the facilitated tracking model of enhancer-promoter communication. Indeed, this model postulates that PolII bound to the enhancer is able to bring it to the promoter via looping of an intervening DNA fragment that should occur in the course of transcription elongation.…”

“…There is strong evidence for the participation of CTCF in the formation of TAD borders. 9,11,17 This may be a consequence of separate TAD assembly by self-compaction of extruded DNA loops. [18][19][20] The "loop extrusion" model postulates that TADs in mammalian genomes could be formed due to the energy-dependent pulling of the chromatin fiber through the "extrusion machine" resulting in the loop formation between convergent CTCF-binding sites (CBS) within this machine and folding of the looped fragment into a TAD (Fig.…”

Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data

“…В последние годы с использованием технологий Hi-C и родственных методов получены новые знания об особенностях трёхмерной архитектуры (укладки) генома человека в интерфазном ядре клетки, влияющих на регуляцию экспрессии генов [7,8,9]. Рассматриваются вопросы формирования топологических доменов, выделения петель, формируемых контактами когезина и фактора CTCF [10]. Для обработки большого объёма данных ChIA-PET и Hi-C, развиваются компьютерные инструменты анализа, позволяющие получить качественно новую информацию о различных аспектах структурной организации генома [11].…”

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

“…Global analysis of long-range chromatin interactions using Hi-C has been achieved at kilobase resolution but requires billions of sequencing reads [8]. High-resolution analysis of long-range chromatin interactions at selected genomic regions can be attained cost-effectively through either ChIA-PET [7,9] or targeted capture and sequencing of Hi-C libraries [10]. ChIA-PET has been used to identify long-range interactions at promoters and enhancers at high resolution in various cell types and species [11].…”

“…To reduce the amount of input materials and improve the sensitivity and robustness of the assay, we developed Proximity Ligation-Assisted ChIP-seq (PLAC-seq), in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation ( Figure 1A, Supplementary information, Figure S1A and Data S1). We demonstrated that by switching the order of proximity ligation and chromatin shearing steps, PLAC-seq greatly improves the efficiency and accuracy over ChIA-PET [7,9] in detection of long-range chromatin interactions in mammalian cells.…”